Evaluation of T-cell response against predicted neoantigens for a patient treated with the CSF-470 vaccine

PODAZA, ENRIQUE; CARRI, IBEL; ARIS, MARIANA; YANKILEVICH, PATRICIO; NIELSEN, MORTEN; MORDOH, JOSÉ; BARRIO, MARÍA MARCELA

México D.F.

Otro; IUIS-ALAI-Mexico-ImmunoInformatics; 2019

Immunopaedia

The CSF-470 vaccine consists of lethally irradiated cells derived from four cutaneous melanoma cell lines established in-house, administered with BCG and GM-CSF as adjuvants. In a phase II clinical trial, the well tolerated vaccine prolonged significantly the distant metastasis-free survival of high-risk patients with very good quality of life. In order to deepen our understanding of the mechanism of action of the vaccine we studied if vaccination induced an immune response against patient-specific neoantigens (neoAgs) as well as against tumor associated antigens (TAAs) shared with the vaccine cells. To that aim, whole exome sequencing (WES) of a sub-cutaneous metastasis and of peripheral blood mononuclear cells from a selected patient was performed, and somatic mutations were obtained. Also, tumor RNASeq was performed and complete HLA haplotype was obtained from patient´s DNA. To predict potential neoAgs derived from these mutations we developed a new pipeline based on predicted MHC binding affinity, stability of peptide-MHC complex, similarity between wild type (wt) and mutant peptides. Candidate peptides were synthesized (>98% purity) for testing. INFγ production in response to stimulation with predicted neoAgs was assessed by ELISPOT in PRE and POST vaccination peripheral blood mononuclear cell samples (P1, P2 and P3 corresponding to 6, 12 and 25 months of treatment). In addition, we also evaluated cellular immune response against shared non-mutated TAAs class I and class II HLA restricted peptides, selected from the TANTIGEN database.Based on self-similarity and predicted affinity to MHC molecules, we created two groups of peptides, those in which the mutant peptide has a higher affinity (group A) vs wt and those in which affinity was the same for mutant and wt but they have a very low similarity (group B). We evaluated 49 peptides of group A and 24 peptides of group B. First, in a screening phase, we assessed 6 pools (A1-A6) of 8-9 peptides each (group A) and 4 pools (B1-B4) of 6 peptides each (group B). We were able to detect INFγ spots just in 4 pools (A1, A3, A5 and A6). Then we evaluated the response to each peptide of the positive pools separately. We found INFγ production in: 2 peptides from A1, 2 from A3, 2 from A5 and 3 from A6. Regarding the TAAs, we observed INFγ production in response to most of the peptides assessed (either class I or class II). To summarize, we observed a relevant immune response against 9 predicted neoAgs from group A and a positive response against a wide range of TAAs. It should be noted that INFγ response against 7/9 neoAgs was found only after vaccination and that the number of spots quantified for TAAs increases progressively from PRE to P3 samples.In conclusion, our results suggest that the proposed new pipeline allows the identification of patient-specific neoAgs, whose exposure and consequent recognition by the immune system appears to be induced by CSF-470 vaccination. Given the powerful and progressing response induced by the TAAs expressed in the vaccine and patient´s tumor we hypothesize that the vaccine could be promoting the phenomenon of epitope spreading. In other words, an initial response against TAAs expressed in the vaccine induces a response against the autologous tumor preventing melanoma relapse.